On May 22, 2003, Venture purchased WVBX-LP (channel 39) in Easton from Vision 3 Broadcasting,[11] a station that a year earlier had been granted a construction permit to upgrade to class A service and move to channel 15 from a transmitter in the Helderberg Mountains in New Scotland, in effect moving WVBX to Albany.[12] Venture took channel 39 off-the-air that June,[13] built the channel 15 facility, gave it the call letters WNYA-CA on June 30, 2003,[14] and announced that the station would serve as a WNYA repeater;[15] this created the unusual circumstance of a repeater station older than its parent station, as WVBX had signed on in 1997 as part of a network of low-power stations based at WVBG-LP (channel 25) in Albany,[16] which itself served as the Capital District's UPN affiliate from 1998 until the launch of "WEDG-TV" in 2000.[17][18]

On September 1, 2003, WNYA launched using the branding "UPN Capital Region."[15] The main signal, WNYA, had an analog transmitter northwest of Pittsfield on Berry Mountain. It became the first full-powered, over-the-air UPN affiliate in the Capital District. In addition to UPN programming, WNYA occasionally carried CBS programming preempted by WRGB, including US Open telecasts that conflicted with WRGB's broadcast of the Jerry Lewis MDA Labor Day Telethon.[15]

On January 24, 2006, The WB and UPN announced that they would end broadcasting and merge to form a new network, The CW; the new network immediately named WEWB-TV (channel 45, now WCWN) its Capital District affiliate after then-owner Tribune Broadcasting signed a ten-year affiliation deal with the new network on most of its WB stations.[19] On February 22, News Corporation announced that it would start up another new broadcast television network called MyNetworkTV; on March 9, it was announced that WNYA would join this network.[20] After having not branded with a channel number during its UPN affiliation, the station chose to call itself "My TV 4 Albany" after its channel position on Time Warner Cable systems. Ironically, nowhere in Berkshire County, Massachusetts is WNYA currently on channel 4; in North Adams, that channel is the spot where Boston's CBS affiliate WBZ-TV is located. After MyNetworkTV's launch on September 5, 2006, WNYA aired the last two weeks of UPN programming from 1 to 3 in the morning from Tuesday to Saturday.

A few months after the affiliation change, on December 5, 2006, Freedom Communications purchased WCWN from Tribune, in effect giving it control over three stations in the Capital District.[21] In February 2007, the joint sales agreement with WRGB was terminated,[15] and WNYA moved to a facility in Rotterdam that formerly housed WMHT-FM-TV.[22]

In December 2007, WNYA reached an agreement to carry the New York Yankees' over-the-air television package, which had previously been carried on WXXA-TV.[23] The station hired Dan Murphy, a former WTEN (channel 10) sports anchor and WOFX (980 AM) host, to host a local pregame show for Yankee telecasts and other local sports broadcasts.[22] Yankee broadcasts remained on WNYA through the 2012 season, after which they migrated to WCWN and WRGB.[24]

On April 18, 2008, WNYA launched its high definition channel on Time Warner Cable in Albany, even though it was not able to transmit digitally until 2009. This coincided with the first Yankee baseball broadcast it had the rights to. WNYA switched to digital broadcasting as part of the transition on June 12, 2009. The Albany repeater, WNYA-CA, has a construction permit to perform a "flash-cut" to a low-power digital signal; due to its Class A status, it is not mandated to make the transition until 2015. Around April 20, 2011, WNYA launched its first digital subchannel in the form of Tribune Broadcasting's Antenna TV over Channel 51.2. The new subchannel also began to be simulcast on WNYA-CA in place of WNYA's main programming.[25]

On February 25, 2013, Hubbard Broadcasting announced that it would purchase WNYA to form a duopoly with its local NBC affiliate WNYT, for $2.3 million, pending FCC approval. Hubbard sought a failed station waiver to acquire the station;[26][27] Venture had put WNYA up for sale in 2009, but no other potential buyers came forward.[28] The sale did not include class-A station WNYA-CA, which remained with Venture Technologies.[29] Under a clause of the sale of WNYA that required WNYA-CA to use a new call sign that does not feature the letters "N" or "Y,"[27] that station became WEPT-CA on March 8, 2013.[14] On May 29, 2013, the FCC approved the sale of WNYA to Hubbard, with Venture retaining ownership of WEPT-CA.[30] The sale was consummated on July 15.[31] WEPT-CA dropped its simulcast of WNYA-DT2 and switched to AMGTV in September 2013, ending its association with WNYA.[32]

On April 17, 2006, WRGB began producing an hour-long 7 a.m. newscast on WNYA.[34] The newscast moved to WCWN shortly after Freedom's purchase of that station.[21]

With Hubbard's acquisition of WNYA, the company indicated that it would eventually produce newscasts on the station with an increased emphasis on news from Berkshire County.[28] WNYT once operated a Berkshire County bureau in Pittsfield but closed it following the 2008 recession.[35] The newscast premiered September 16, 2013 and is known on-air as NewsChannel 13 Live at 10 on My 4 Albany.[36] The show airs weeknights for a half hour in a fast-paced format and includes a "Berkshire Moment" segment featuring western Massachusetts headlines powered by The Berkshire Eagle.[37] It competes with the firmly established sixty minute broadcast seen every night on WXXA (produced by WTEN) and another thirty minute news show on WCWN (a weeknight-only production by WRGB).